The microbial world, generally invisible to the naked eye, has
largely shaped our environment and has been instrumental in
the emergence and evolution of all other living organisms
on Earth. These microscopic unicellular organisms were for
3 billion years the only forms of life on our planet.
Their most spectacular action was the modification of the
primitive atmosphere: the dioxygen certainly not present
initially reached its present concentration (21 % of the gas
content of the atmosphere) through the action of microorganisms that are able of oxygenic photosynthesis. For the
evolution of life, it is now widely accepted that extremely
complex multicellular life forms have emerged from eukaryote microorganisms classified in the kingdom Plantae and in
the Stramenopiles and Opisthokonta (especially metazoans
which includes humans). These life forms are still dependent
on the activity of microorganisms.
If a disaster, whether natural or caused by humans, should
annihilate all nonmicrobial living species, it is likely that
some microorganisms that have colonized all oceans (from
the surface to the abyssal domain) and the earth’s crust (to a
depth of hundreds of meters) would be spared and would
allow the initiation of a new evolution process, whatever the
new environmental conditions at the end of this disaster,
except in the absence of liquid water.
The activity of the biosphere as a whole is totally dependent on the action of microorganisms. The major goal of
microbial ecology (which, in general, can be defined as the
study of microorganisms in natural and anthropized
ecosystems) is to improve our understanding of:
1. Their origin and evolution
The first inhabitants of the Earth, microorganisms have
developed mechanisms that allowed them to adapt to all
climatic and geological changes that have occurred on the
Earth since the origin of life. They are actually present in all
habitats and are able to adapt to the most extreme conditions
of life in terms of temperature, pressure, pH, salinity, radiation, etc.
To explain the longevity and ubiquity of microorganisms,
it is important to take into account the very short duration of
their cell cycle, their high mutation rates and adaptability to
environmental changes, their extraordinary metabolic plasticity that allows them to adapt to a large diversity of carbon
and energy sources that are available in their environment
(including xenobiotics, which are molecules produced by
humans), the diversity as well as the frequency of genetic
information transfer between populations and communities,
and their ability to survive under starvation conditions and
all resistance strategies to face environmental stresses. This
resistance can involve morphological and metabolic changes
such as the production of detoxifying enzymes, DNA repair
mechanisms, and the production of resistance forms
(endospores, cysts, etc.). In addition, their small size results
in a very high surface/volume ratio and therefore in a high
exchange capacity with the external environment. This
capacity promotes their ubiquity in natural environments
(Woese 1987).
2. Their taxonomic and functional diversities and their
abundance and distribution in ecosystems
The microbial ecologist is led to inventory microorganisms in the environment, which means all prokaryotic
and eukaryotic unicellular microorganisms but also viruses
in their functional dimension. The microbial compartment is
a component of all ecosystems, similar to the animal or
plant components. In addition to this taxonomic diversity,
microbial ecologists have to describe the functions that
microorganisms are in charge of, which means understanding which genes are involved and expressed in situ
(Brock 1966).
3. Their role in the functioning of ecosystems and in particular that of biogeochemical cycles
Due to their important biomass, metabolic diversity, and
capacity to adapt to the environment, microorganisms play a
major role in the organization, functioning, and evolution of
ecosystems. They are both producers, consumers, and decomposers, and they participate in all stages of the organic and
mineral matter transformation, and they are alone to perform
some transformation processes. Their role is also essential in
the functioning of food webs. In the absence of plants and
animals, biogeochemical cycles could continue to operate
based solely on the activity of microorganisms. The study of
their role in the different cycles requires the description,
location, and quantification of microbial populations and
communities that are involved, as well as the characterization
of all organic matter degradation and synthesis pathways and
the measurement of their activities. On this last point, it is
important to note that if the action of microorganisms proceed
at the microenvironment scale, the impact of their activities
apply at the earth scale (Fenchel et al. 2000).
4. The interactions between microorganisms and between
microorganisms and plants, animals and humans
All together, these interactions which are in most cases
positive (beneficial) or negative (adverse) are classified as
biotic interactions. In the environment, microorganisms do
not live alone: they form populations often grouped into
communities and can form highly structured assemblages
such as biofilms or microbial mats. From the first stages of
life, microorganisms have assembled to form multilayer
structures called stromatolites which are microbial mats
made with autotrophic and heterotrophic prokaryotes and
fossilized for millions of years. The success of these
associations is quite exceptional: if they have appeared
more than 3 billion years ago, the stromatolites are still
present. Studies of biotic interactions must take into account
not only the interactions between microorganisms but also
their interactions with multicellular organisms such as
plants, animals, and humans (Margulis 1981).
5. Interactions between microorganisms and their environment, considered as abiotic interactions
4
J.-C. Bertrand et al.
largely shaped our environment and has been instrumental in
the emergence and evolution of all other living organisms
on Earth. These microscopic unicellular organisms were for
3 billion years the only forms of life on our planet.
Their most spectacular action was the modification of the
primitive atmosphere: the dioxygen certainly not present
initially reached its present concentration (21 % of the gas
content of the atmosphere) through the action of microorganisms that are able of oxygenic photosynthesis. For the
evolution of life, it is now widely accepted that extremely
complex multicellular life forms have emerged from eukaryote microorganisms classified in the kingdom Plantae and in
the Stramenopiles and Opisthokonta (especially metazoans
which includes humans). These life forms are still dependent
on the activity of microorganisms.
If a disaster, whether natural or caused by humans, should
annihilate all nonmicrobial living species, it is likely that
some microorganisms that have colonized all oceans (from
the surface to the abyssal domain) and the earth’s crust (to a
depth of hundreds of meters) would be spared and would
allow the initiation of a new evolution process, whatever the
new environmental conditions at the end of this disaster,
except in the absence of liquid water.
The activity of the biosphere as a whole is totally dependent on the action of microorganisms. The major goal of
microbial ecology (which, in general, can be defined as the
study of microorganisms in natural and anthropized
ecosystems) is to improve our understanding of:
1. Their origin and evolution
The first inhabitants of the Earth, microorganisms have
developed mechanisms that allowed them to adapt to all
climatic and geological changes that have occurred on the
Earth since the origin of life. They are actually present in all
habitats and are able to adapt to the most extreme conditions
of life in terms of temperature, pressure, pH, salinity, radiation, etc.
To explain the longevity and ubiquity of microorganisms,
it is important to take into account the very short duration of
their cell cycle, their high mutation rates and adaptability to
environmental changes, their extraordinary metabolic plasticity that allows them to adapt to a large diversity of carbon
and energy sources that are available in their environment
(including xenobiotics, which are molecules produced by
humans), the diversity as well as the frequency of genetic
information transfer between populations and communities,
and their ability to survive under starvation conditions and
all resistance strategies to face environmental stresses. This
resistance can involve morphological and metabolic changes
such as the production of detoxifying enzymes, DNA repair
mechanisms, and the production of resistance forms
(endospores, cysts, etc.). In addition, their small size results
in a very high surface/volume ratio and therefore in a high
exchange capacity with the external environment. This
capacity promotes their ubiquity in natural environments
(Woese 1987).
2. Their taxonomic and functional diversities and their
abundance and distribution in ecosystems
The microbial ecologist is led to inventory microorganisms in the environment, which means all prokaryotic
and eukaryotic unicellular microorganisms but also viruses
in their functional dimension. The microbial compartment is
a component of all ecosystems, similar to the animal or
plant components. In addition to this taxonomic diversity,
microbial ecologists have to describe the functions that
microorganisms are in charge of, which means understanding which genes are involved and expressed in situ
(Brock 1966).
3. Their role in the functioning of ecosystems and in particular that of biogeochemical cycles
Due to their important biomass, metabolic diversity, and
capacity to adapt to the environment, microorganisms play a
major role in the organization, functioning, and evolution of
ecosystems. They are both producers, consumers, and decomposers, and they participate in all stages of the organic and
mineral matter transformation, and they are alone to perform
some transformation processes. Their role is also essential in
the functioning of food webs. In the absence of plants and
animals, biogeochemical cycles could continue to operate
based solely on the activity of microorganisms. The study of
their role in the different cycles requires the description,
location, and quantification of microbial populations and
communities that are involved, as well as the characterization
of all organic matter degradation and synthesis pathways and
the measurement of their activities. On this last point, it is
important to note that if the action of microorganisms proceed
at the microenvironment scale, the impact of their activities
apply at the earth scale (Fenchel et al. 2000).
4. The interactions between microorganisms and between
microorganisms and plants, animals and humans
All together, these interactions which are in most cases
positive (beneficial) or negative (adverse) are classified as
biotic interactions. In the environment, microorganisms do
not live alone: they form populations often grouped into
communities and can form highly structured assemblages
such as biofilms or microbial mats. From the first stages of
life, microorganisms have assembled to form multilayer
structures called stromatolites which are microbial mats
made with autotrophic and heterotrophic prokaryotes and
fossilized for millions of years. The success of these
associations is quite exceptional: if they have appeared
more than 3 billion years ago, the stromatolites are still
present. Studies of biotic interactions must take into account
not only the interactions between microorganisms but also
their interactions with multicellular organisms such as
plants, animals, and humans (Margulis 1981).
5. Interactions between microorganisms and their environment, considered as abiotic interactions
4
J.-C. Bertrand et al.